void BayesGraphLoad::set_data( Graph& graph,
const std::string cndFileName,
const std::string dataVecFileName ) const {
std::ifstream obsFile(dataVecFileName.c_str());
assert(obsFile); // todo: throws instead
samogwas::CSVIterator<int> obsLine(obsFile);
size_t index = 0;
for( ; obsLine != samogwas::CSVIterator<int>(); ++obsLine ) {
auto row = std::make_shared<Vec>(obsLine->size(), 0);
for (unsigned i = 0; i < obsLine->size(); ++i) {
(*row)[i] = obsLine->at(i);
}
graph[index++].set_data_vec(row, true);
}
obsFile.close();
std::ifstream cndFile(cndFileName.c_str());
if (cndFile) {
samogwas::CSVIterator<double> cndLine(cndFile);
for( ; cndLine != samogwas::CSVIterator<double>(); ++cndLine ) {
auto row = std::make_shared<RealVec>(cndLine->size(), 0);
for (unsigned i = 0; i < cndLine->size(); ++i) {
(*row)[i] = cndLine->at(i);
}
graph[index++].set_cnd_obs_vec(row, false);
}
cndFile.close();
}
}
void Observation::loadObservations(string filename){
cout << "load Observations start\n";
string obsFilename = filename + ".input";
ifstream obsFile(obsFilename.c_str());
char * buffer = new char[2];
vector <unsigned int>* currentSeq = new vector<unsigned int>();
sequences.push_back(currentSeq);
char peek = obsFile.peek();
while (!obsFile.eof()){
while (peek != '\n' && !obsFile.eof()){
if (isWhiteSpace(peek)){
if (peek != '\n'){
obsFile.read(buffer, 1); // consume whitespace
}
}
else{
string s;
obsFile >> s;
int i = mapObsToInt(s);
currentSeq->push_back(i);
//cout << t << " " << i << "\n";
}
peek = obsFile.peek();
}
int size = currentSeq->size();
obsFile.read(buffer, 1); // consume newline
peek = obsFile.peek();
if (!obsFile.eof()){
currentSeq = new vector<unsigned int>();
sequences.push_back(currentSeq);
}
}
obsFile.close();
cout << "load Observations end\n";
}